Vegetable crops provide a rich source of essential nutrients for humanity and represent critical economic values to global rural societies. However, genetic studies of vegetable crops have lagged behind major food cro...Vegetable crops provide a rich source of essential nutrients for humanity and represent critical economic values to global rural societies. However, genetic studies of vegetable crops have lagged behind major food crops, such as rice, wheat and maize,thereby limiting the application of molecular breeding. In the past decades, genome sequencing technologies have been increasingly applied in genetic studies and breeding of vegetables. In this review, we recapitulate recent progress on reference genome construction, population genomics and the exploitation of multi-omics datasets in vegetable crops. These advances have enabled an in-depth understanding of their domestication and evolution, and facilitated the genetic dissection of numerous agronomic traits, which jointly expedites the exploitation of state-of-the-art biotechnologies in vegetable breeding. We further provide perspectives of further directions for vegetable genomics and indicate how the ever-increasing omics data could accelerate genetic, biological studies and breeding in vegetable crops.展开更多
Low-temperature(LT)stress threatens cucumber production globally;however,the molecular mechanisms underlying LT tolerance in cucumber remain largely unknown.Here,using a genome-wide association study(GWAS),we found a ...Low-temperature(LT)stress threatens cucumber production globally;however,the molecular mechanisms underlying LT tolerance in cucumber remain largely unknown.Here,using a genome-wide association study(GWAS),we found a naturally occurring single nucleotide polymorphism(SNP)in the STAYGREEN(CsSGR)coding region at the gLTT5.1 locus associated with LT tolerance.Knockout mutants of CsSGR generated by clustered regularly interspaced palindromic repeats(CRISPR)/CRISPR-associated nuclease 9 exhibit enhanced LT tolerance,in particularly,increased chlorophyll(Chl)content and reduced reactive oxygen species(ROS)accumulation in response to LT.Moreover,the C-repeat Binding Factor 1(CsCBF1)transcription factor can directly activate the expression of CsSGR.We demonstrate that the LT-sensitive haplotype CsSGRHapA,but not the LT-tolerant haplotype CsSGR^(HapG)could interact with NON-YELLOW COLORING 1(CsNYC1)to mediate Chl degradation.Geographic distribution of the CsSGR haplotypes indicated that the CsSGR^(HapG)was selected in cucumber accessions from high latitudes,potentially contributing to LT tolerance during cucumber cold-adaptation in these regions.CsSGR mutants also showed enhanced tolerance to salinity,water deficit,and Pseudoperonospora cubensis,thus CsSGR is an elite target gene for breeding cucumber varieties with broad-spectrum stress tolerance.Collectively,our findings provide new insights into LT tolerance and will ultimately facilitate cucumber molecular breeding.展开更多
Rare genetic variants are abundant in genomes but less tractable in genome-wide association study. Here we exploit a strategy of rare variation mapping to discover a gene essential for tendril development in cucumber ...Rare genetic variants are abundant in genomes but less tractable in genome-wide association study. Here we exploit a strategy of rare variation mapping to discover a gene essential for tendril development in cucumber (Cucumis sativus L.). In a collection of 〉3000 lines, we discovered a unique tendril-less line that forms branches instead of tendrils and, therefore, loses its climbing ability. We hypothesized that this unusual phenotype was caused by a rare variation and subsequently identified the causative single nucleotide poly- morphism. The affected gene TEN encodes a TCP transcription factor conserved within the cucurbits and is expressed specifically in tendrils, representing a new organ identity gene. The variation occurs within a pro- tein motif unique to the cucurbits and impairs its function as a transcriptional activator. Analyses of transcrip- tomes from near-isogenic lines identified downstream genes required for the tendril's capability to sense and climb a support. This study provides an example to explore rare functional variants in plant genomes.展开更多
基金supported by the National Natural Science Foundation of China(31991180,31922076,32130093)the National Key Research and Development Program of China(2019YFA0906200,2021YFF1000100)+4 种基金the Agricultural Science and Technology Innovation Program(CAAS-ZDRW202101)Guangdong Major Project of Basic and Applied Basic Research(2021B0301030004)the Special Funds for Science Technology Innovation and Industrial Development of Shenzhen Dapeng New District(RC201901-05)Shenzhen Outstanding Talents Training Fund,the Shenzhen Science and Technology Program(KQTD2016113010482651)the“Taishan Scholar”Foundation of the People’s Government of Shandong Province,Yunnan Science Fund(202105AF150028,202005AE160015)。
文摘Vegetable crops provide a rich source of essential nutrients for humanity and represent critical economic values to global rural societies. However, genetic studies of vegetable crops have lagged behind major food crops, such as rice, wheat and maize,thereby limiting the application of molecular breeding. In the past decades, genome sequencing technologies have been increasingly applied in genetic studies and breeding of vegetables. In this review, we recapitulate recent progress on reference genome construction, population genomics and the exploitation of multi-omics datasets in vegetable crops. These advances have enabled an in-depth understanding of their domestication and evolution, and facilitated the genetic dissection of numerous agronomic traits, which jointly expedites the exploitation of state-of-the-art biotechnologies in vegetable breeding. We further provide perspectives of further directions for vegetable genomics and indicate how the ever-increasing omics data could accelerate genetic, biological studies and breeding in vegetable crops.
基金supported by the National Natural Science Foundation of China (No. 32372704)Key-Area Research and Development Program of Guangdong Province (2020B020220001)+2 种基金Beijing Joint Research Program for Germplasm Innovation and New Variety Breeding (G20220628003-03)the Earmarked Fund for Modern Agroindustry Technology Research System (CARS-23)Science and Technology Innovation Program of the Chinese Academy of Agricultural Science (CAAS-ASTIP-IVFCAAS)
文摘Low-temperature(LT)stress threatens cucumber production globally;however,the molecular mechanisms underlying LT tolerance in cucumber remain largely unknown.Here,using a genome-wide association study(GWAS),we found a naturally occurring single nucleotide polymorphism(SNP)in the STAYGREEN(CsSGR)coding region at the gLTT5.1 locus associated with LT tolerance.Knockout mutants of CsSGR generated by clustered regularly interspaced palindromic repeats(CRISPR)/CRISPR-associated nuclease 9 exhibit enhanced LT tolerance,in particularly,increased chlorophyll(Chl)content and reduced reactive oxygen species(ROS)accumulation in response to LT.Moreover,the C-repeat Binding Factor 1(CsCBF1)transcription factor can directly activate the expression of CsSGR.We demonstrate that the LT-sensitive haplotype CsSGRHapA,but not the LT-tolerant haplotype CsSGR^(HapG)could interact with NON-YELLOW COLORING 1(CsNYC1)to mediate Chl degradation.Geographic distribution of the CsSGR haplotypes indicated that the CsSGR^(HapG)was selected in cucumber accessions from high latitudes,potentially contributing to LT tolerance during cucumber cold-adaptation in these regions.CsSGR mutants also showed enhanced tolerance to salinity,water deficit,and Pseudoperonospora cubensis,thus CsSGR is an elite target gene for breeding cucumber varieties with broad-spectrum stress tolerance.Collectively,our findings provide new insights into LT tolerance and will ultimately facilitate cucumber molecular breeding.
文摘Rare genetic variants are abundant in genomes but less tractable in genome-wide association study. Here we exploit a strategy of rare variation mapping to discover a gene essential for tendril development in cucumber (Cucumis sativus L.). In a collection of 〉3000 lines, we discovered a unique tendril-less line that forms branches instead of tendrils and, therefore, loses its climbing ability. We hypothesized that this unusual phenotype was caused by a rare variation and subsequently identified the causative single nucleotide poly- morphism. The affected gene TEN encodes a TCP transcription factor conserved within the cucurbits and is expressed specifically in tendrils, representing a new organ identity gene. The variation occurs within a pro- tein motif unique to the cucurbits and impairs its function as a transcriptional activator. Analyses of transcrip- tomes from near-isogenic lines identified downstream genes required for the tendril's capability to sense and climb a support. This study provides an example to explore rare functional variants in plant genomes.